Key camp question: Who will spell Bowman?

The 49ers have ranked among top three in points allowed the past three years, but one of the NFL’s most formidable defenses figures to be absent two All-Pros to start the season.

Outside linebacker Aldon Smith is expected to serve as NFL suspension of unknown length, while inside linebacker NaVorro Bowman (knee) will miss about half the season. The 49ers figure to replace Smith with Dan Skuta and Corey Lemonier, the tandem they used last year when Smith missed five games to receive treatment for a substance-abuse problem.

It’s not as clear who will replace Bowman.

Michael Wilhoite, who took the first-string snaps in the offseason, is the front-runner entering camp and is the only candidate with NFL starting experience.

An undrafted free agent from Division II Washburn University, Wilhoite capably spelled Patrick Willis for two games last year. He had 20 tackles and the 49ers allowed one touchdown in wins over the Rams and Texans.

In the spring, however, the 49ers drafted some competition for Wilhoite when they selected Wisconsin’s Chris Borland in the third round. Despite lacking ideal size or speed, Borland (5-11, 248) left Wisconsin as a first-team All-American who had the second-most forced fumbles (15) in FBS history.

“I understand why there are some doubting Thomases with him,” defensive coordinator Vic Fangio said in June. “I totally understand that. And they may end up being right. But this guy’s got such good instincts. For the safety and inside linebacker position, instincts need to be at the top of the list when you’re evaluating them and he’s very strong there.”

The competition also includes Nick Moody and Shayne Skov. Moody, a 2013 sixth-round pick, missed eight games as a rookie with a broken hand. Skov, who surprisingly went undrafted in May, has familiarity with the 49ers defense after playing for Fangio in 2010 at Stanford.